The chief Guantanamo war crimes prosecutor, Army Brig. Gen. Mark Martins, and an aide pose for a CBS crew inside the war court built for the conspiracy trial of accused 9/11 mastermind Khalid Sheik Mohammed during a September visit, in this screen grab from a "60 Minutes" episode that aired Nov. 3, 2013.

The chief Guantanamo war crimes prosecutor, Army Brig. Gen. Mark Martins, and an aide pose for a CBS crew inside the war court built for the conspiracy trial of accused 9/11 mastermind Khalid Sheik Mohammed during a September visit, in this screen grab from a "60 Minutes" episode that aired Nov. 3, 2013.

The FBI is investigating something related to the Sept. 11 case, but it’s not the release of alleged 9/11 mastermind Khalid Sheik Mohammed’s commentary to The Huffington Post, a special war-court prosecutor wrote a military judge Monday.

U.S. Attorney Fernando Campoamor-Sánchez added in a nine-page filing provided to the Miami Herald by the U.S. Department of Justice, that the government specifically kept Sept. 11 trial prosecutors in the dark about what he calls a “preliminary investigation.”

“The FBI Preliminary Investigation does not pertain to the disclosure of Mr. Mohammad’s written communications to third parties,” Campoamor-Sánchez wrote Army Col. James L. Pohl in the notice that seeks 30 additional days to flesh out more details.

The filing does not make clear what the FBI is investigating. Instead, Campoamor-Sánchez wrote, he gave the judge a second, classified document to describe “the nature of the actual FBI Preliminary Investigation being conducted.” Neither the defense attorneys nor the case prosecutors can read it.

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Any wider disclosure, he wrote, would “jeopardize an ongoing FBI criminal investigation.”

The murky issue stalled preparations for a Sept. 11 trial during hearings last week after a defense attorney for accused 9/11 plotter Ramzi bin al Shibh announced that two FBI agents surreptitiously questioned a classification specialist assigned to his team.

The FBI agents were asking questions about some of the Sept. 11 defense attorneys, including how the Huffington Post got a copy of Mohammed’s unclassified 36-page “Invitation to Happiness” — musings by the self-described former al-Qaida chief of operations on American culture. The agents also asked the bin al Shibh defense team member to sign a nondisclosure agreement with the FBI, which defense lawyers cast as a bid to enlist him as a confidential informant.

a conflict?

Defense lawyers, who already work under a strict security regime because their clients were previously interrogated by the CIA, protested to the judge that FBI was apparently spying on their work. Such behavior, they argued, could create a conflict of interest if not a chilling effect as they prepare for the death-penalty prosecution of Mohammed and four alleged accomplices related to the Sept. 11, 2001 attacks that killed nearly 3,000 people in New York, Pennsylvania and the Pentagon.

Pohl adjourned the proceedings until June to probe the possible conflict, as well as whether defense team strategy has been compromised.

Defense lawyers want the judge to question a tribunal prosecutor who was absent from last week’s proceedings, Joanna Baltes, who recently left the Justice Department’s counter-terrorism section for work as chief of staff in the office of the FBI’s deputy director. Baltes is still a member of the Sept. 11 prosecution team but has skipped several hearings.

As a first step, Campoamor-Sánchez advised the judge that the FBI kept 9/11 prosecutors out of the ongoing probe.

“There is nothing to indicate thus far that any documents or information collected from the FBI’s Preliminary Investigation have been shared with the Prosecution Team,” he wrote.

In a footnote Campoamor-Sánchez defines the trigger for an FBI preliminary investigation: “Any ‘allegation or information’ indicative of possible criminal activity or threats to the national security.”

Defense attorney Jim Harrington said that the filing raised new questions about whether a conflict exists.

Now with Mohammed’s “Invitation to Happiness” commentary no longer at issue, said Harrington, a seasoned criminal defense attorney from Buffalo, the Sept. 11 defense teams were “back to the drawing board” and “wondering what the investigation is about.”

One scenario raised by some 9/11 defense attorneys last week, two years after the case began with arraignment, is that some might have to step down and be replaced if they feel threatened by the investigation.

Either way, the judge authorized the Chief Defense Counsel, Air Force Col. Karen Mayberry, to assign two new lawyers to bin al Shibh and Mohammed to advise them on the legal implications of the possible conflict.

The federal prosecutor noted in his filing that, if investigators are reading privileged communications between the former CIA captives and their American military and civilian lawyers, there’s a system in place to do it secretly — so case prosecutors won’t learn trial strategy.